rs10494554

Variant names:

• chr1-183146754-T-G
• rs10494554

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0893 in 152,228 control chromosomes in the GnomAD database, including 1,534 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.089 (1534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13568 AN: 152110 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0764

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0893 AC: 13592 AN: 152228 Hom.: 1534 Cov.: 32 AF XY: 0.0892 AC XY: 6643 AN XY: 74448

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.0469

Gnomad4 FIN AF: 0.00348

Gnomad4 NFE AF: 0.00595

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0513 Hom.: 117

Bravo AF: 0.105

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10494554; hg19: chr1-183115889;